ArticlemedRxiv : the preprint server for health sciences2022
Genomic epidemiology reveals the impact of national and international restrictions measures on the SARS-CoV-2 epidemic in Brazil.
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Article in medRxiv : the preprint server for health sciences, 2022. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Not yet cited in PubMed.
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103 authors.
Marta GiovanettiLaboratório de Flavivírus, Fundação Oswaldo Cruz, Rio de Janeiro, Brazil.
Svetoslav Nanev SlavovUniversity of São Paulo, Ribeirão Preto Medical School, Blood Center of Ribeirão Preto, Ribeirão Preto, SP, Brazil.
Vagner FonsecaLaboratório de Flavivírus, Fundação Oswaldo Cruz, Rio de Janeiro, Brazil.
Eduan WilkinsonKwaZulu-Natal Research Innovation and Sequencing Platform (KRISP), School of Laboratory Medicine and Medical Sciences, College of Health Sciences, University of KwaZulu-Natal, Durban, South Africa.
Houriiyah TegallyKwaZulu-Natal Research Innovation and Sequencing Platform (KRISP), School of Laboratory Medicine and Medical Sciences, College of Health Sciences, University of KwaZulu-Natal, Durban, South Africa.
José Salvatore Leister PatanéButantan Institute, São Paulo, Brazil.
Vincent Louis VialaButantan Institute, São Paulo, Brazil.
James Emmanuel SanKwaZulu-Natal Research Innovation and Sequencing Platform (KRISP), School of Laboratory Medicine and Medical Sciences, College of Health Sciences, University of KwaZulu-Natal, Durban, South Africa.
Evandra Strazza RodriguesUniversity of São Paulo, Ribeirão Preto Medical School, Blood Center of Ribeirão Preto, Ribeirão Preto, SP, Brazil.
Elaine Vieira SantosUniversity of São Paulo, Ribeirão Preto Medical School, Blood Center of Ribeirão Preto, Ribeirão Preto, SP, Brazil.
Flavia AburjaileLaboratório de Genética Celular e Molecular, Instituto de Ciências Biológicas, Universidade Federal de Minas Gerais, Belo Horizonte, Minas Gerais, Brazil.
Joilson XavierLaboratório de Flavivírus, Fundação Oswaldo Cruz, Rio de Janeiro, Brazil.
Hegger FritschLaboratório de Flavivírus, Fundação Oswaldo Cruz, Rio de Janeiro, Brazil.
Talita Emile Ribeiro AdelinoLaboratório de Flavivírus, Fundação Oswaldo Cruz, Rio de Janeiro, Brazil.
Felicidade PereiraLaboratorio Central de Saude Publica da Bahia-LACEN-BA, Salvador, Bahia, Brazil.
Arabela LealLaboratorio Central de Saude Publica da Bahia-LACEN-BA, Salvador, Bahia, Brazil.
Felipe Campos de Melo IaniLaboratório Central de Saúde Pública do Estado de Minas Gerais, Fundac ão Ezequiel Dias, Belo Horizonte, Minas Gerais, Brazil.
Glauco de Carvalho PereiraLaboratório Central de Saúde Pública do Estado de Minas Gerais, Fundac ão Ezequiel Dias, Belo Horizonte, Minas Gerais, Brazil.
Cynthia VazquezLaboratorio Central de Salud Pública, Asunción, Paraguay.
Gladys Mercedes Estigarribia SanabriaUniversidad Nacional del Caaguazú, Instituto Regional de Investigación en Salud.
Elaine Cristina de OliveiraLaboratório Central de Saúde Pública do Estado de Mato Grosso, Cuiabá, Brazil.
Luiz DemarchiLaboratório Central de Saúde Pública do Estado de Mato Grosso do Sul, Campo Grande, Mato Grosso do Sul, Brazil.
Julio CrodaUniversidade Federal de Mato Grosso do Sul.
Rafael Dos Santos BezerraUniversity of São Paulo, Ribeirão Preto Medical School, Blood Center of Ribeirão Preto, Ribeirão Preto, SP, Brazil.
Loyze Paola Oliveira de LimaButantan Institute, São Paulo, Brazil.
Antonio Jorge MartinsButantan Institute, São Paulo, Brazil.
Claudia Renata Dos Santos BarrosButantan Institute, São Paulo, Brazil.
Elaine Cristina MarquezeButantan Institute, São Paulo, Brazil.
Jardelina de Souza Todao BernardinoButantan Institute, São Paulo, Brazil.
Debora Botequio MorettiButantan Institute, São Paulo, Brazil.
Ricardo Augusto BrassalotiUniversity of São Paulo, Centro de Genômica Funcional da ESALQ, Piracicaba, SP, Brazil.
Raquel de Lello Rocha Campos CassanoUniversity of São Paulo, Centro de Genômica Funcional da ESALQ, Piracicaba, SP, Brazil.
Pilar Drummond Sampaio Corrêa MarianiNGS Soluções Genômicas, Piracicaba, SP, Brazil.
João Paulo KitajimaMendelics Análise Genômica.
Bibiana SantosMendelics Análise Genômica.
Rodrigo Proto-SiqueiraInstituto de Biologia Molecular, Laboratório Antonello, Rio Grande do Sul, Brazil.
Vlademir Vicente CantarelliUniversidade Federal de Ciências da Saúde de Porto Alegre (UFCSPA), Universidade Feevale, Grupo Exame Laboratórios, Rio Grande do Sul, Brazil.
Stephane TostaLaboratório de Genética Celular e Molecular, Instituto de Ciências Biológicas, Universidade Federal de Minas Gerais, Belo Horizonte, Minas Gerais, Brazil.
Vanessa Brandão NardyLaboratorio Central de Saude Publica da Bahia-LACEN-BA, Salvador, Bahia, Brazil.
Luciana Reboredo de Oliveira da SilvaLaboratorio Central de Saude Publica da Bahia-LACEN-BA, Salvador, Bahia, Brazil.
Marcela Kelly Astete GómezLaboratorio Central de Saude Publica da Bahia-LACEN-BA, Salvador, Bahia, Brazil.
Jaqueline Gomes LimaLaboratorio Central de Saude Publica da Bahia-LACEN-BA, Salvador, Bahia, Brazil.
Adriana Aparecida RibeiroLaboratório Central de Saúde Pública do Estado de Minas Gerais, Fundac ão Ezequiel Dias, Belo Horizonte, Minas Gerais, Brazil.
Natália Rocha GuimarãesLaboratório Central de Saúde Pública do Estado de Minas Gerais, Fundac ão Ezequiel Dias, Belo Horizonte, Minas Gerais, Brazil.
Luiz Takao WatanabeLaboratório Central de Saúde Pública do Estado de Mato Grosso, Cuiabá, Brazil.
Luana Barbosa Da SilvaLaboratório Central de Saúde Pública do Estado de Mato Grosso, Cuiabá, Brazil.
Raquel da Silva FerreiraLaboratório Central de Saúde Pública do Estado de Mato Grosso, Cuiabá, Brazil.
Mara Patricia F da PenhaVigilância em Saúde do Estado de Mato Grosso, Cuiabá, Brazil.
María José OrtegaLaboratorio Central de Salud Pública, Asunción, Paraguay.
Andrea Gómez de la FuenteLaboratorio Central de Salud Pública, Asunción, Paraguay.
Shirley VillalbaLaboratorio Central de Salud Pública, Asunción, Paraguay.
Juan ToralesLaboratorio Central de Salud Pública, Asunción, Paraguay.
María Liz GamarraLaboratorio Central de Salud Pública, Asunción, Paraguay.
Carolina AquinoLaboratorio Central de Salud Pública, Asunción, Paraguay.
Gloria Patricia Martínez FigueredoUniversidad Nacional del Caaguazú, Instituto Regional de Investigación en Salud.
Wellington Santos FavaUniversidade Federal de Mato Grosso do Sul.
Ana Rita C Motta-CastroUniversidade Federal de Mato Grosso do Sul.
James VenturiniUniversidade Federal de Mato Grosso do Sul.
Sandra Maria do Vale Leone de OliveiraUniversidade Federal de Mato Grosso do Sul.
Crhistinne Cavalheiro Maymone GonçalvesSecretaria de Saúde do Estado do Mato Grosso do Sul.
Maria do Carmo Debur RossaLaboratório Central do Estado do Paraná (Lacen/PR).
Guilherme Nardi BeckerLaboratório Central do Estado do Paraná (Lacen/PR).
Mayra Marinho PresibellaLaboratório Central do Estado do Paraná (Lacen/PR).
Nelson Quallio MarquesLaboratório Central do Estado do Paraná (Lacen/PR).
Irina Nastassja RiedigerLaboratório Central do Estado do Paraná (Lacen/PR).
Sonia RaboniHospital de Clínicas da Universidade Federal do Paraná, Curitiba, PR.
Gabriela Mattoso CoelhoLaboratório de Virologia Molecular - Instituto Carlos Chagas/Fiocruz PR, Curitiba, PR.
Allan Henrique Depieri CataneoLaboratório de Virologia Molecular - Instituto Carlos Chagas/Fiocruz PR, Curitiba, PR.
Camila ZanlucaLaboratório de Virologia Molecular - Instituto Carlos Chagas/Fiocruz PR, Curitiba, PR.
Claudia N Duarte Dos SantosLaboratório de Virologia Molecular - Instituto Carlos Chagas/Fiocruz PR, Curitiba, PR.
Patricia Akemi AssatoSão Paulo State University (UNESP), School of Agricultural Sciences, Department of Bioprocesses and Biotechnology, Botucatu, Brazil.
Felipe Allan da Silva da CostaSão Paulo State University (UNESP), School of Agricultural Sciences, Department of Bioprocesses and Biotechnology, Botucatu, Brazil.
Mirele Daiana PoletiDepartment of Veterinary Medicine, School of Animal Science and Food Engineering, University of Sao Paulo, Pirassununga, São Paulo, Brazil.
Jessika Cristina Chagas LesbonDepartment of Veterinary Medicine, School of Animal Science and Food Engineering, University of Sao Paulo, Pirassununga, São Paulo, Brazil.
Elisangela Chicaroni MattosDepartment of Veterinary Medicine, School of Animal Science and Food Engineering, University of Sao Paulo, Pirassununga, São Paulo, Brazil.
Cecilia Artico BanhoLaboratório de Pesquisas em Virologia, Departamento de Doenças Dermatológicas, Infecciosas e Parasitárias, Faculdade de Medicina de São José do Rio Preto.
Lívia SacchettoLaboratório de Pesquisas em Virologia, Departamento de Doenças Dermatológicas, Infecciosas e Parasitárias, Faculdade de Medicina de São José do Rio Preto.
Marília Mazzi MoraesLaboratório de Pesquisas em Virologia, Departamento de Doenças Dermatológicas, Infecciosas e Parasitárias, Faculdade de Medicina de São José do Rio Preto.
Rejane Maria Tommasini GrottoSão Paulo State University (UNESP), School of Agricultural Sciences, Department of Bioprocesses and Biotechnology, Botucatu, Brazil.
Jayme A Souza-NetoSão Paulo State University (UNESP), School of Agricultural Sciences, Department of Bioprocesses and Biotechnology, Botucatu, Brazil.
Maurício Lacerda NogueiraLaboratório de Pesquisas em Virologia, Departamento de Doenças Dermatológicas, Infecciosas e Parasitárias, Faculdade de Medicina de São José do Rio Preto.
Heidge FukumasuDepartment of Veterinary Medicine, School of Animal Science and Food Engineering, University of Sao Paulo, Pirassununga, São Paulo, Brazil.
Luiz Lehmann CoutinhoUniversity of São Paulo, Centro de Genômica Funcional da ESALQ, Piracicaba, SP, Brazil.
Rodrigo Tocantins CaladoUniversity of São Paulo, Ribeirão Preto Medical School, Blood Center of Ribeirão Preto, Ribeirão Preto, SP, Brazil.
Raul Machado NetoButantan Institute, São Paulo, Brazil.
Ana Maria Bispo de FilippisLaboratório de Flavivírus, Fundação Oswaldo Cruz, Rio de Janeiro, Brazil.
Rivaldo Venancio da CunhaFundação Oswaldo Cruz, Bio-Manguinhos, Rio de Janeiro, Rio de Janeiro, Brazil.
Carla FreitasCoordenação Geral de Laboratórios de Saúde Pública/Secretaria de Vigilância em Saúde, Ministério da Saúde (CGLAB/SVS-MS) Brasília, Distrito Federal, Brazil.
Cassio Roberto Leonel PeterkaCoordenação Geral das Arboviroses, Secretaria de Vigilaçncia em Saúde/Ministério da Saúde (CGARB/SVS-MS), Brasília, Distrito Federal, Brazil.
Cássia de Fátima Rangel FernandesDepartamento de Imunização e Doenças Transmissíveisa/Secretaria de Vigilância em Saúde, Ministério da Saúde, Brasília, Distrito Federal, Brazil.
Wildo Navegantes de AraújoOrganização Pan-Americana da Saúde/Organização Mundial da Saúde, Brasília, Distrito Federal, Brazil.
Rodrigo Fabiano do Carmo SaidOrganização Pan-Americana da Saúde/Organização Mundial da Saúde, Brasília, Distrito Federal, Brazil.
Maria AlmironOrganização Pan-Americana da Saúde/Organização Mundial da Saúde, Brasília, Distrito Federal, Brazil.
Carlos Frederico Campelo de Albuquerque E MeloOrganização Pan-Americana da Saúde/Organização Mundial da Saúde, Brasília, Distrito Federal, Brazil.
José LourençoDepartment of Zoology, Peter Medawar Building, University of Oxford, Oxford, UK.
Tulio de OliveiraKwaZulu-Natal Research Innovation and Sequencing Platform (KRISP), School of Laboratory Medicine and Medical Sciences, College of Health Sciences, University of KwaZulu-Natal, Durban, South Africa.
Edward C HolmesSydney Institute for Infectious Diseases, School of Life and Environmental Sciences and School of Medical Sciences, University of Sydney, Sydney, NSW, Australia.
Ricardo HaddadButantan Institute, São Paulo, Brazil.
Sandra Coccuzzo SampaioButantan Institute, São Paulo, Brazil.
Maria Carolina EliasButantan Institute, São Paulo, Brazil.
Simone KashimaUniversity of São Paulo, Ribeirão Preto Medical School, Blood Center of Ribeirão Preto, Ribeirão Preto, SP, Brazil.
Luiz Carlos Junior de AlcantaraLaboratório de Flavivírus, Fundação Oswaldo Cruz, Rio de Janeiro, Brazil.
Dimas Tadeu CovasUniversity of São Paulo, Ribeirão Preto Medical School, Blood Center of Ribeirão Preto, Ribeirão Preto, SP, Brazil.
Funding
University of Washington Arboviral Research Network (UWARN)U01AI151698 · NIAID · UNIVERSITY OF WASHINGTON · PI Michael Gale, PETER MACGARR RABINOWITZ · 2020 to 2026
$13.3MCoordinating Research on Emerging Arboviral Threats Encompassing the Neotropics II (CREATE-NEO II)U01AI151807 · NIAID · UNIVERSITY OF TEXAS MED BR GALVESTON · PI Kathryn Alyce Hanley, MAURICIO Lacerda NOGUEIRA · 2020 to 2026
$9.8MNIAID NIH HHS U01 AI151698NIAID NIH HHS U01 AI151807
Abstract
Brazil has experienced some of the highest numbers of COVID-19 cases and deaths globally and from May 2021 made Latin America a pandemic epicenter. Although SARS-CoV-2 established sustained transmission in Brazil early in the pandemic, important gaps remain in our understanding of virus transmission dynamics at the national scale. Here, we describe the genomic epidemiology of SARS-CoV-2 using near-full genomes sampled from 27 Brazilian states and a bordering country - Paraguay. We show that the early stage of the pandemic in Brazil was characterised by the co-circulation of multiple viral lineages, linked to multiple importations predominantly from Europe, and subsequently characterized by large local transmission clusters. As the epidemic progressed under an absence of effective restriction measures, there was a local emergence and onward international spread of Variants of Concern (VOC) and Variants Under Monitoring (VUM), including Gamma (P.1) and Zeta (P.2). In addition, we provide a preliminary genomic overview of the epidemic in Paraguay, showing evidence of importation from Brazil. These data reinforce the usefulness and need for the implementation of widespread genomic surveillance in South America as a toolkit for pandemic monitoring that provides a means to follow the real-time spread of emerging SARS-CoV-2 variants with possible implications for public health and immunization strategies.
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